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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ggtaactgtttattgttttccaaatttaaattattacctttggatttatcacactttcgaatgtcaaatatgctgtgctcataggattgcacattgaattttacaGGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATTTTCTGGTCCAAGGTGGGAAGCTCTAGTTAAAAAGGGGGCCAAGAAGCAA

Basic information

species Glycine max
transcript GLYMA18G53700.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G53700.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0150g00190.t01 (Vitis vinifera), 3'ss of exon 5
ggtaactgtttattgttttccaaatttaaattattacctttggatttatcacactttcgaatgtcaaatatgctgtgctca-taggattgcacattga-attttacaGGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATTTTCTGGTCCAAGGTGGGAAGCTCTAGTTAAAAAGGGGGCCAAGAAGCAA-
                       | | || | |||  |  |  | || |||  |||| ||  ||  || |  | |  |  | ||  || | || || | || ||  |||| || ||||| ||||||||| |||| |||||||||||||| | |||||| ||||| || || ||||||||||| || || || || |||||||| ||  
---------------------gtaataaattaatttacaatcaaattgtcatccttttgagggtttaaaactcaggacctaatatcatgggacttttatatgttctagGCTGCAGTAGCTCAAGCAGCACTGGCATACCAGCTCTACCAGAAGAAATTCTCTGGGCCTAGATGGGAAGCTCTGGTGAAGAAAGGTGCCAAGAAACAGA
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|7041883|gb|AW471777.1|AW471777
EST:     AAGGCCCTTGAGAAAATTGGCACCCCAGTGGCCCTTAATCTACGCGGGAA                         GGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT
genomic: AAGGCCCTTGAGAAAATTGGCACCCCAGTGGCCCTTAATCTACGCGGGAAggtaactgtt ... gaattttacaGGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT
EST: gi|58017240|gb|CX703982.1|CX703982
EST:     AAGGCCCTTGAGAAAATTGGCACCCCAGTGGCCCTTAATCTACGCGGGAA                         GGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT
genomic: AAGGCCCTTGAGAAAATTGGCACCCCAGTGGCCCTTAATCTACGCGGGAAggtaactgtt ... gaattttacaGGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT
EST: gi|254347696|gb|GR853945.1|GR853945
EST:     AAGGCCCTTGAGAAAATTGGCACCCCAGTGGCCCTTAATCTACGCGGGAA                         GGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT
genomic: AAGGCCCTTGAGAAAATTGGCACCCCAGTGGCCCTTAATCTACGCGGGAAggtaactgtt ... gaattttacaGGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT
EST: gi|298186515|gb|HO037148.1|HO037148
EST:     GAGGCCCTTGAGAAAATTGGCACCCCAGTGGCCCTTAATCTACGCGGGAA                         GGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT
genomic: AAGGCCCTTGAGAAAATTGGCACCCCAGTGGCCCTTAATCTACGCGGGAAggtaactgtt ... gaattttacaGGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT
EST: gi|19452834|gb|BM954244.1|BM954244
EST:     AAGGCCCTTGAGAAAATTGGCACCCCAGTGGCCCTTAATCTACGCGGGAA                         GGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT
genomic: AAGGCCCTTGAGAAAATTGGCACCCCAGTGGCCCTTAATCTACGCGGGAAggtaactgtt ... gaattttacaGGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT
EST: gi|151398727|gb|EV268598.1|EV268598
EST:     AAGGCCCTTGAGAAAATTGGCACCCCAGTGGCCCTTAATCTACGCGGGAA                         GGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT
genomic: AAGGCCCTTGAGAAAATTGGCACCCCAGTGGCCCTTAATCTACGCGGGAAggtaactgtt ... gaattttacaGGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT
EST: gi|58014569|gb|CX701311.1|CX701311
EST:     AAGGCCCTTGAGAAAATTGGCACCCCAGTGGCCCTTAATCTACGCGGGAA                         GGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT
genomic: AAGGCCCTTGAGAAAATTGGCACCCCAGTGGCCCTTAATCTACGCGGGAAggtaactgtt ... gaattttacaGGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT
EST: gi|58018609|gb|CX705351.1|CX705351
EST:     AAGGCCCTTGAGAAAATTGGCACCCCAGTGGCCCTTAATCTACGCGGGAA                         GGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT
genomic: AAGGCCCTTGAGAAAATTGGCACCCCAGTGGCCCTTAATCTACGCGGGAAggtaactgtt ... gaattttacaGGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT
EST: gi|58017437|gb|CX704179.1|CX704179
EST:     AAGGCCCTTGAGAAAATTGGCACCCCAGTGGCCCTTAATCTACGCGGGAA                         GGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT
genomic: AAGGCCCTTGAGAAAATTGGCACCCCAGTGGCCCTTAATCTACGCGGGAAggtaactgtt ... gaattttacaGGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT
EST: gi|308098810|gb|HO760651.1|HO760651
EST:     AAGGCCCTTGAGAAAATTGGCACCCCAGTGGCCCTTAATCTACGTGGGAA                         GGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT
genomic: AAGGCCCTTGAGAAAATTGGCACCCCAGTGGCCCTTAATCTACGCGGGAAggtaactgtt ... gaattttacaGGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT
EST: gi|298196531|gb|HO041274.1|HO041274
EST:     AAGGCCCTTGAGAAAATTGGCACCCCAGTGGCCCTTAATCTACGCGGGAA                         GGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTA
genomic: AAGGCCCTTGAGAAAATTGGCACCCCAGTGGCCCTTAATCTACGCGGGAAggtaactgtt ... gaattttacaGGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTA
EST: gi|5175583|gb|AI759916.1|AI759916
EST:     AAGGCCCTTGAGAAAATTGGCACCCCAGTGGCCCTTAATCTACGCGGGAA                         GGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT
genomic: AAGGCCCTTGAGAAAATTGGCACCCCAGTGGCCCTTAATCTACGCGGGAAggtaactgtt ... gaattttacaGGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT
EST: gi|6846407|gb|AW348697.1|AW348697
EST:     AAGGCCCTTGAGAAAATTGGCACCCCAGTGGCNNNTAATCTACGCGNNNA                         GGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT
genomic: AAGGCCCTTGAGAAAATTGGCACCCCAGTGGCCCTTAATCTACGCGGGAAggtaactgtt ... gaattttacaGGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT
EST: gi|254347695|gb|GR853944.1|GR853944
EST:     AAGGCCCTTGAGAAAATTGGCACCCCAGTGGCCCTTAATCTACGCGGGAA                         GGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT
genomic: AAGGCCCTTGAGAAAATTGGCACCCCAGTGGCCCTTAATCTACGCGGGAAggtaactgtt ... gaattttacaGGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT
EST: gi|58023410|gb|CX710151.1|CX710151
EST:     AAGGCCCTTGAGAAAATTGGCACCCCAGTGGCCCTTAATCTACGCGGGAA                         GGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT
genomic: AAGGCCCTTGAGAAAATTGGCACCCCAGTGGCCCTTAATCTACGCGGGAAggtaactgtt ... gaattttacaGGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT
EST: gi|298172256|gb|HO021848.1|HO021848
EST:     AAGGCCCTTGAGAAAATTGGCACCCCAGTGGCCCTTAATCTACGCGGGAA                         GGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT
genomic: AAGGCCCTTGAGAAAATTGGCACCCCAGTGGCCCTTAATCTACGCGGGAAggtaactgtt ... gaattttacaGGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT
EST: gi|208242597|gb|GE038795.1|GE038795
EST:     CTTAATCTACGCGGGAA                         GGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT
genomic: CTTAATCTACGCGGGAAggtaactgtt ... gaattttacaGGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT
EST: gi|298191275|gb|HO038754.1|HO038754
EST:     AAGGCCCTTGAGAAAATTGGCACCCCAGTGGCCCTTAATCTACGCGGGAA                         GGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT
genomic: AAGGCCCTTGAGAAAATTGGCACCCCAGTGGCCCTTAATCTACGCGGGAAggtaactgtt ... gaattttacaGGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acactttcgaatgtcaaatatgctgtgctcataggattgcacattgaattttacaGGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATTTTCTGGTCCAAGGTGGGAAGCTCTAGTTAAAAAGGGGGCCAAGAAGCAA
                                          attgaatttta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtaactgtttattgttttccaaatttaaattattacctttggatttatcacactttcgaatgtcaaatatgctgtgctcataggattgcacattgaattttacaGGCAGCGGTAGCCCAAGCAGCATTGGCTTACCAGCTCTACCAAAGGAAATTTTCTGGTCCAAGGTGGGAAGCTCTAGTTAAAAAGGGGGCCAAGAAGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA